The advent of combinatorial chemistry and high throughput screening techniques has revolutionized the drug discovery process allowing for screening and generation of small molecule lead compounds against molecular targets at an unprecedented rate. Most screening assays for small molecule compounds are target driven and it is often difficult to control for off-target interactions. However, the potential interaction of drugs with unintended targets or pathways could prove fatal leading to toxicity or side effects. Additionally, in phenotype-based screening where the target is not readily apparent, identification of the target can prove elusive. Therefore, there is an increasing need in drug discovery, and chemical biology for technologies that can predict or provide information allowing for testable hypotheses regarding the underlying mechanism of action of small molecule compounds.
A number of multi-dimensional profiling technologies including gene expression profiling, proteomic profiling, protein-fragment complementation profiling, high content microscopy-based profiling and cell line cytotoxicity based profiling approaches have been described to measure both the interaction of compounds on intended targets and also generate testable hypotheses concerning mechanism of action and off-target effects. In all cases a very large information-rich data set is generated which can be used to cluster compounds based on activity patterns. Each data point in such a data set corresponds to the measured value for one particular assay target, with all the data in the set being measured at the same time point. These information-rich data sets can be mined with the help of specially designed algorithms to look for specific patterns of activity amongst the compounds being screened and to formulate hypothesis concerning the mechanism of action of compounds. Indeed, all the profiling approaches have had various degrees of success not only in elucidating mechanism of action of unknown compounds, but also unraveling new and novel mechanisms for existing drugs. The challenge in implementing multi-dimensional profiling technologies in a drug discovery setting is to formulate a method that is practical, simple to use and easy to analyze and can be used on routine basis.